Just a thought, for if you wanted to "remove" windows as well. If you aren't worried about ever needing them, you could change the opaqueness (background) to zero. Make sure it's set for zero upon mouseover as well. Remove any frames and titlebars, and checkmark the option to clickthrough. Basically, you will make the window invisible, and you will be able to use your mouse as if it's no longer there.
However, the risk of doing that is, you will have to restore to default if you ever need the window in the future. Unless you know exactly where the window is, and right click exactly the right spot. And in the case of temporary windows, click at the right time as well. I mean, I've done it, and it does work. But sometimes you might find a "ghost" showing up because some little bit of information that the window provides becomes shown.
Darq has made things a lot easier though, even allowing you to move around ghost windows for temporary windows that are very difficult to otherwise place. He has a windows manager as well, that allows you to have a drop down option window. With that, you can quickly locate all windows that you want to get rid of, and alter their settings, if it's possible to get rid of them. Darq has made extensive changes to both default and custom elements, so it's well worth checking out everything and learning what works how, before making final decisions.
Increase the peace, decrease the chaos.